Adenomatous polyposis coli (APC) and KRAS proto-oncogene (KRAS) mutations frequently co-occur in non-small cell lung cancer. Inactivating APC mutations in colorectal carcinoma has been well characterized, leading to the approaches targeting on dysregulated APC pathway. However, it remains undetermined whether such approaches are also applicable to non-small cell lung cancer patients harboring similar mutations of APC. Dickkopf-related protein 2 (DKK2) is a Wnt antagonist. Our previous study has proved that anti-DKK2 antibody 5F8 suppressed the growth of colorectal carcinoma with APC mutations, illustrating a new target agent of APC-mutated tumors. This study aimed to investigate the potential of applying anti-DKK2 antibody to non-small cell lung cancer with APC mutations. We found significant upregulation of Dkk2 expression in APC-mutated lung cancers. Administration of DKK2 antibody inhibited cancer growth via modulating tumor immune microenvironment in lung cancer mouse models. Our study provided strong evidence supporting APC mutations-directed applications of anti-DKK2 targeted therapy in a wide range of cancer types, including lung cancer.

HPV oropharyngeal cancers have now surpassed cervical cancer rates in the US. Dental providers' engagement in HPV education and vaccination efforts may help reduce the burden of HPV oropharyngeal cancers. We examined factors associated with oral health students' willingness to train and administer the human papillomavirus (HPV) vaccine in dental settings. US students in 15 oral health programs participated in an online survey in 2016. Unadjusted and adjusted multivariable logistic regression were conducted and odds ratios (OR) and 95% confidence intervals (CI) were reported. Analyses were conducted in SAS Version 9.4. Data from a total of N = 306 students were analyzed to examine sociodemographic, educational, practice, and attitudinal factors associated with willingness to train and administer the HPV vaccine. Majority of the participants were female (70.3%), non-Hispanic/Latino (90.8%), and White (62.1%). Perceiving that HPV vaccination recommendation (OR = 1.95, 95% CI = 1.14-3.35) and administration (OR = 3.79, 95% CI = 1.63-8.81) was in the dental professional's scope was positively associated with outcome measures when other factors were held constant. Students with greater patient contact time (OR = 4.47, 95% CI = 1.14-17.58) and lower role conflict (agreed that HPV vaccine administration was in the dental professional's scope) had higher odds of willingness to administer the HPV vaccine when other factors were held constant (OR = 5.9, 95% CI = 2.27-15.3). The major barrier to engaging oral health students in HPV vaccination efforts was role conflict. Professional organizations and oral health programs should strongly support the role of oral health professionals in HPV oropharyngeal prevention.

To analyse the homogeneous and heterogeneous risk factors for occurrence and prognosis in lung cancer patients diagnosed with bone metastasis (BM) by using the Surveillance, Epidemiology, and End Results (SEER) database.

Considered as one of the major epidemics of the 21st century, osteoporosis affects approximately 200 million people globally, with significant worldwide impact on rates of morbidity and mortality and massive socioeconomic burdens. Mainly characterized by decreased bone mineral density (BMD) and increased risk of bone fragility/deterioration, this devastating silent epidemic typically has no symptoms until a fracture occurs. The multifactorial disease, osteoporosis is instigated by complex interactions between genetic, metabolic and environmental factors, with severe impact on the biomechanics of the musculoskeletal system. This article provides a review of the epidemiology, genetic and biomechanical aspects of primary osteoporosis. The review begins with a summary of the epidemiology and global prevalence of osteoporosis. Sections 1 and 2 discuss the genetic associations and molecular signaling pathways involved in normal and pathological osteogenesis while Section 3 explores the biomechanics of osteoporosis and its quantitative damaging effects on critical bone mechanical properties, and associated bone remodeling. Overall, this review summarizes the recent findings about osteoporosis and emphasizes the importance of an integrative holistic approach in investigating osteoporosis towards providing better informed, more effective preventive and treatment modalities. Importantly, this work also explores the limited available literature on the various aspects of osteoporosis in the United Arab Emirates (UAE), Gulf Cooperation Council (GCC), and Middle East despite its alarming prevalence in the region, and highlights the need for further research and studies taking into consideration the importance of the vitamin D receptor (VDR) gene influencing the development of osteoporosis.

This work presented the sequences of activated sludge from two municipal wastewater treatment plants (WWTPs) located in a high altitude Plateau in Tibet, China (∼3650 m above the sea level). Sequencing data are the 16S rRNA gene amplicons of V4-V5 region that sequenced on an Illumina HiSeq PE250 platform. Data presented here include detail description and water quality parameters of the WWTPs as well as results of 16S rRNA gene sequences from their active sludges. The core microbial communities in the WWTPs were shown at the taxonomic level of phylum, class, order, family, genus and species. The sequencing data have been deposited in NCBI BioProject PRJNA477990 with the Biosample accessions SAMN09488330-SAMN09488338. The annotation of OTU table at the genus level was assessable on Zenodo (https://zenodo.org/record/2105899#.XA0vQPZuJyw).

This article contains the uptake data of two reducible antigen-adjuvant conjugates with different sensitivities to the extracellular and intracellular reductive environment. Using a linker with different redox sensitivity the adjuvant cytosine-phosphate-guanine (CpG) was conjugated to the fluorescently labeled model tumour antigen ovalbumin (OVA). The uptake of the conjugates by dendritic cells in a total splenocyte culture was determined using flow cytometry. The data presented in this paper supports the finding in the research article "Intracellular cleavable CpG oligodeoxynucleotide - antigen conjugate enhances anti-tumour immunity" (Kramer et al., 2016) [1].

In this data paper we share the absorption spectrum of Ag NP ablated in pure water and in presence of trisodium citrate (TSC). We also share the full emission spectrum of the irradiation lamp used for the reshaping process described in the related research paper. The data is related to the research article "Plasmon Sensing and enhancement of laser prepared silver colloids" [1].

PGC-1β is a transcriptional co-activator of nuclear receptors, which acts to increase energy expenditure. PGC-1β fused to GAL4 DNA-binding domain transfected in HEK293T cells showed a reporter luciferase activity. We screened food-derived and natural compounds using a reporter assay system to measure the transcriptional activity of PGC-1β. We found that soy-derived isoflavones, genistein and daidzein, and several resveratrols activated PGC-1β, see "Genistein, daidzein, and resveratrols stimulate PGC-1β-mediated gene expression" [1]. The list of 166 compounds and their reporter activity is shown here.

The data and analyses presented support the research article entitled "Coupling partial-equilibrium and dynamic biogenic carbon models to assess future transport scenarios in France" (Albers et al., 2019). Carbon sequestration and storage in forestry products (e.g. transport fuels) is sought as a climate change mitigation option. The data presented support and inform dynamic modelling approaches to predict biomass growth and carbon fixation dynamics, of a tree or forest stand, over specific rotation lengths. Data consists of species-specific yield tables, parameters for non-linear growth models and allometric equations. Non-linear growth models and allometric equations are listed and described. National statistics and surveys of the wood supply chain serve to identify main tree species, standing wood volumes and distributions within specific geographies; here corresponding to managed forests in France. All necessary data and methods for the computation of the annual fixation flows are presented.

Background: Norovirus, also known as the winter vomiting bug, is the predominant cause of non-bacterial gastroenteritis worldwide. Disease control is predicated on a robust innate immune response during the early stages of infection. Double-stranded RNA intermediates generated during viral genome replication are recognised by host innate immune sensors in the cytoplasm, activating the strongly antiviral interferon gene programme. Ifit proteins (interferon induced proteins with tetratricopeptide repeats), which are highly expressed during the interferon response, have been shown to directly inhibit viral protein synthesis as well as regulate innate immune signalling pathways. Ifit1 is well-characterised to inhibit viral translation by sequestration of eukaryotic initiation factors or by directly binding to the 5' terminus of foreign RNA, particularly those with non-self cap structures. However, noroviruses have a viral protein, VPg, covalently linked to the 5' end of the genomic RNA, which acts as a cap substitute to recruit the translation initiation machinery. Methods: Ifit1 knockout RAW264.7 murine macrophage-like cells were generated using CRISPR-Cas9 gene editing. These cells were analysed for their ability to support murine norovirus infection, determined by virus yield, and respond to different immune stimuli, assayed by quantitative PCR. The effect of Ifit proteins on norovirus translation was also tested in vitro. Results: Here, we show that VPg-dependent translation is completely refractory to Ifit1-mediated translation inhibition in vitro and Ifit1 cannot bind the 5' end of VPg-linked RNA. Nevertheless, knockout of Ifit1 promoted viral replication in murine norovirus infected cells. We then demonstrate that Ifit1 promoted interferon-beta expression following transfection of synthetic double-stranded RNA but had little effect on toll-like receptor 3 and 4 signalling. Conclusions: Ifit1 is an antiviral factor during norovirus infection but cannot directly inhibit viral translation. Instead, Ifit1 stimulates the antiviral state following cytoplasmic RNA sensing, contributing to restriction of norovirus replication.

Ovarian cancer is an intra-abdominal tumor in which the presence of ascites facilitates metastatic dissemination, and associated with poor prognosis. However, the significance of metabolic alterations in ovarian cancer cells in the ascites microenvironment remains unclear. Here we show ovarian cancer cells exhibited increased aggressiveness in ascites microenvironment via reprogramming of lipid metabolism. High lipid metabolic activities are found in ovarian cancer cells when cultured in the ascites microenvironment, indicating a metabolic shift from aerobic glycolysis to β-oxidation and lipogenesis. The reduced AMP-activated protein kinase (AMPK) activity due to the feedback effect of high energy production led to the activation of its downstream signaling, which in turn, enhanced the cancer growth. The combined treatment of low toxic AMPK activators, the transforming growth factor beta-activated kinase 1 (TAK1) and fatty acid synthase (FASN) inhibitors synergistically impair oncogenic augmentation of ovarian cancer. Collectively, targeting lipid metabolism signaling axis impede ovarian cancer peritoneal metastases.

Polyacrylamides (PAM) are widely used as water-soluble polymers producing gel in oil reservoirs to assist in oil extraction from reservoirs with high levels of heterogeneity. These gels are susceptible to degradation due to hydrolysis in harsh reservoir conditions such as elevated temperature and salinity. This study uses a polymer integration technique in attempting to optimize the performance of PAM in the enhanced oil recovery process for reservoirs with high temperature and salinity. The results show that, at high temperature, hydrolysis is suppressed and gel stability is maintained via the addition of Polyvinylpyrrolidone (PVP) to PAM solutions. The optimum composition was identified as being 20/80 wt% PAM: PVP for oilfield operations at 90 °C and a moderate salinity of 43,280 ppm. The degree of hydrolysis at 30 days was suppressed from 75% to 29.9%, with associated increases in viscosity from 11 to 38.2 mPa.s and from 18 to 44.3 mPa.s corresponding to rotational speeds of 30 and 10 rpm respectively. The issue of high salinity was considered by increasing the salinity of the optimised PAM: PVP mixture to 200,000 ppm. Under these conditions the degree of hydrolysis of the optimised solution increased from 29.9 to 46.9% and viscosity decreased from 38.2 to 28.6 and from 44.3 to 40.4 mPa.s for rotational speeds of 30 and 10 rpm respectively. 2-Acrylamido-2-MethylpropaneSulfonic acid (AMPS) was added to the mix to try to improve temperature stability. It was observed that, with an optimum composition of 18/72/10 wt% PAM:PVP:AMPS, the degree of hydrolysis decreased to 22% with viscosity levels of 30.6 and 22.8 mPa.s corresponding to rotational speeds of 10 and 30 rpm respectively.

Nowadays, there is an increasing tendency toward using probiotics in different food systems. In this work, probiotic survival, texture features and sensory properties of synbiotic chewing gum containing encapsulated probiotic organisms (Lactobacillus reuteri) were studied. Probiotics were encapsulated using alginate, inulin (0-1%) and lecithin (0-1%). Storage trials showed that, unlike control, the viability of the probiotic in encapsulated samples was retained after 21 days. Probiotic survival was increased by increasing of inulin and lecithin in cell walls. Samples containing encapsulated organisms had different texture parameters compared to the control. Sensory panelists liked the chewing gum with encapsulated lactobacilli. Thus, chewing gum has been shown to be an excellent food for delivery of probiotic lactobacilli. Principal component analysis (PCA) allowed discriminating among probiotics survival and chewing gum specialties. Partial least squares regression (PLSR) models were applied to find out the relationships between sensory and instrumental data.

Osteocytes are long-lived, highly interconnected, terminally differentiated osteoblasts that reside within mineralized bone matrix. They constitute about 95% of adult bone cells and play important functions including in the regulation of bone remodeling, phosphate homeostasis, and mechanical stimuli sensing and response. However, the role of osteocytes in the pathogenesis of congenital diseases of abnormal bone matrix is poorly understood. This study characterized in vivo transcriptional changes in osteocytes from CrtapKO and oim/oim mouse models of osteogenesis imperfecta (OI) compared with wild-type (WT) control mice. To do this, RNA was extracted from osteocyte-enriched cortical femurs and tibias, sequenced and subsequently analyzed to identify differentially expressed transcripts. These models were chosen because they mimic two types of OI with different genetic mutations that result in distinct type I collagen defects. A large number of transcripts were dysregulated in either model of OI, but 281 of them were similarly up- or downregulated in both compared with WT controls. Conversely, very few transcripts were differentially expressed between the CrtapKO and oim/oim mice, indicating that distinct alterations in type I collagen can lead to shared pathogenic processes and similar phenotypic outcomes. Bioinformatics analyses identified several critical hubs of dysregulation that were enriched in annotation terms such as development and differentiation, ECM and collagen fibril organization, cell adhesion, signaling, regulatory processes, pattern binding, chemotaxis, and cell projections. The data further indicated alterations in important signaling pathways such as WNT and TGF-β but also highlighted new candidate genes to pursue in future studies. Overall, our study suggested that the osteocyte transcriptome is broadly dysregulated in OI with potential long-term consequences at the cellular level, which deserve further investigations. © 2019 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Bone is the most common site of prostate cancer (PC) metastasis. Studies suggest that cancer stem cells (CSCs) are associated with stemness characteristics, providing some support for the concept that CSCs act as osteosclerotic precursors in bone microenvironmental niches. Here, we asked whether ectopic overexpression of CD133 maintains stability of CSCs in human PC cell lines and induces the changes of molecular features in the bone microenvironment. Ectopic overexpression of CD133 in PC3 or DU145 cells led to increased expression of ALDHA1, OCT4, and NANOG, enhanced colony-forming ability, and increased ALDH activity. In addition, micro-CT imaging, confocal microscopy, and H&E staining of mouse tissue confirmed that CD133 overexpression in PC3 and DU145 led to marked osteolytic bone tumor. However, expression of osteoblastic markers such as collagen type I, bone sialoprotein, and osteocalcin (OC) at the tumor margin of CD133-overexpressing PC3 tumors in mouse tibiae was higher than that of CD133-overexpressing DU145 tumors with osteosclerotic molecular features. In addition, expression of osteopontin (OPN) mRNA/protein by CD133-overexpressing PC3 cells was higher than that by DU145 cells. Especially, conditioned medium (CM) from PC3CD133+ cells increased osterix (OSX) activity in bone marrow stromal cells (BMSCs), resulting in increased expression of OC mRNA/protein resulted in increased staining of mineralized matrix by Alizarin red. However, CM from OPN silenced PC3CD133+ cells led to a reduction of OC mRNA and protein expression through OSX activity resulted in reduced amount of mineralized matrix. In conclusion, these findings suggest that CD133 plays a functional role in regulating CSC characteristics in PCs and modulates their abilities in which induce the osteosclerosis of BMSCs. In addition, OPN from CSCs acts as a niche component that promotes osteosclerosis by supporting osteoblastic differentiation of BMSCs.

Restriction-modification (R-M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R-M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R-M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R-M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.

A primary challenge in the analysis of RNA-seq data is to identify differentially expressed genes or transcripts while controlling for technical biases. Ideally, a statistical testing procedure should incorporate the inherent uncertainty of the abundance estimates arising from the quantification step. Most popular methods for RNA-seq differential expression analysis fit a parametric model to the counts for each gene or transcript, and a subset of methods can incorporate uncertainty. Previous work has shown that nonparametric models for RNA-seq differential expression may have better control of the false discovery rate, and adapt well to new data types without requiring reformulation of a parametric model. Existing nonparametric models do not take into account inferential uncertainty, leading to an inflated false discovery rate, in particular at the transcript level. We propose a nonparametric model for differential expression analysis using inferential replicate counts, extending the existing SAMseq method to account for inferential uncertainty. We compare our method, Swish, with popular differential expression analysis methods. Swish has improved control of the false discovery rate, in particular for transcripts with high inferential uncertainty. We apply Swish to a single-cell RNA-seq dataset, assessing differential expression between sub-populations of cells, and compare its performance to the Wilcoxon test.

Controversies exist on the influence of lower pole anatomy (infundibular pelvic angle, IPA; infundibular length, IL; and infundibular width, IW) for success and outcomes related to the treatment of stones in the lower pole. We wanted to look at the role of lower pole anatomy to study clinical outcomes in patients treated for isolated lower pole stones (LPS) using retrograde intra renal surgery (RIRS), and also perform a review to look at the published literature on the influence of pelvicalyceal anatomy on success with RIRS. Data were prospectively collected (June 2013-June 2016) for all patients who underwent RIRS for LPS, and the imaging was then retrospectively reviewed to calculate the IPA, IL and IW using the Elbahnasy method. A systematic review was also conducted for all English language articles between January 2000 and April 2018, reporting on the impact of pelvicaliceal anatomy on RIRS. A total of 108 patients with LPS were included with a male to female ratio of 2:3 and a mean age of 54.7 years. The mean lower pole stone size was 9.3 mm (range 3-29 mm) and 102/108 (94.4%) patients were stone free (SF) at the end of their procedure. While steep IPA (< 30°), operative time duration and larger stone size were significant predictors of failure, the placement of ureteric access sheath, IW and IL did not influence treatment outcomes. Six studies (460 patients) met the inclusion criteria for our review. The IPA, IW, IL for failure ranged from 26° to 38°, 5.5-7 mm and 24-34 mm, respectively. The SFR ranged from 78 to 88% with a metaanalysis showing IPA as the most important predictor of treatment outcomes for LPS. Infundibular pelvic angle seems to be the most important predictor for the treatment of LPS using RIRS. Pelvicalyceal anatomy in conjunction with stone size and hardness seem to dictate the success, and decisions on the type of surgical interventions should reflect this.

In the era of combined antiretroviral therapy, HIV-1 infected individuals are living longer lives; however, longevity is met with an increasing number of HIV-1 associated neurocognitive disorders (HAND) diagnoses. The transactivator of transcription (Tat) is known to mediate the neurotoxic effects in HAND by acting directly on neurons and also indirectly via its actions on glia. The Go/No-Go (GNG) task was used to examine HAND in the Tat transgenic mouse model. The GNG task involves subjects discriminating between two stimuli sets in order to determine whether or not to inhibit a previously trained response. Data reveal inhibitory control deficits in female Tat(+) mice (p = .048) and an upregulation of cannabinoid type 1 receptors (CB1R) in the infralimbic (IL) cortex in the same female Tat(+) group (p < .05). A significant negative correlation was noted between inhibitory control and IL CB1R expression (r = -.543, p = .045), with CB1R expression predicting 30% of the variance of inhibitory control (R2 = .295, p = .045). Furthermore, there was a significant increase in spontaneous excitatory postsynaptic current (sEPSC) frequencies in Tat(+) compared to Tat(-) mice (p = .008, across sexes). The increase in sEPSC frequency was significantly attenuated by bath application of PF3845, a fatty acid amide hydrolase (FAAH) enzyme inhibitor (p < .001). Overall, the GNG task is a viable measure to assess inhibitory control deficits in Tat transgenic mice and results suggest a potential therapeutic treatment for the observed deficits with drugs which modulate endocannabinoid enzyme activity. Graphical Abstract Results of the Go/No-Go operant conditioning task reveal inhibitory control deficits in female transgenic Tat(+) mice without significantly affecting males. The demonstrated inhibitory control deficits appear to be associated with an upregulation of cannabinoid type 1 receptors (CB1R) in the infralimbic (IL) cortex in the same female Tat(+) group.

Infectious bronchitis virus (IBV) affects both vaccinated and unvaccinated flocks worldwide, with a significant impact on the poultry industry. The aim of the present study is to characterize an emerging variant pathogenic IBV originating from field outbreaks in vaccinated Egyptian layer flock. Samples were collected from disease-suspected flock with a history of administration of live and inactivated IBV vaccines (Ma5 type). Virus propagation in embryonated chicken eggs (ECEs), after three successive passages, revealed typical IBV lesions such as curling and dwarfism. The reported isolate was identified by a real-time reverse transcriptase PCR assay targeting nucleocapsid (N) gene and, further characterized by full-length spike (S1) gene sequencing. Phylogenetic analysis revealed clustering of the isolated virus within 4/91 genotype of GI-13 lineage. Deduced amino acid sequences identity revealed 75-76% and 88-90% similarity with the currently used classic (H120, Ma5, and M41) and variant vaccine strains (4/91 and CR88) in Egypt, respectively. Recombination analysis gave an evidence for distinct patterns of origin for the studied isolate providing another example of intra-genotypic recombination among IBVs and the first example of recombination within the GI-13 lineage in the Egyptian field. The studied isolate (IBV/CK/EG/Fadllah-10/2019) emerged as a result of recombination between the variant group (Egy/var I genotype, GI-23 lineage) as a major parent and the CR88 variant vaccine strain (4/91 genotype, GI-13 lineage) as minor parent. Our data suggest that both mutation and recombination may be contributing to the emergence of IBV variants which ascertain the importance of disease monitoring in vaccinated flocks as well as re-appropriation for the current vaccine strategies.